Does "importing key configuration" (shortcuts) only add keys?
A saved key configuration keeps track of added, removed and modified shortcuts. In fact, it is merely storing differences from (changes made to) default configuration. And when reloaded, it re-creates default keymap, and 'replays' stored modifications over it.

This system also allows to support (relatively) well changes in default keymap, without totally breaking or leaving customized one in frozen, old state.